Starting phenix.real_space_refine on Fri Sep 11 17:05:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x5a_33013/09_2026/7x5a_33013.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x5a_33013/09_2026/7x5a_33013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x5a_33013/09_2026/7x5a_33013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x5a_33013/09_2026/7x5a_33013.map" model { file = "/net/cci-nas-00/data/ceres_data/7x5a_33013/09_2026/7x5a_33013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x5a_33013/09_2026/7x5a_33013.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 104 5.49 5 S 32 5.16 5 C 6510 2.51 5 N 1888 2.21 5 O 2152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10686 Number of models: 1 Model: "" Number of chains: 12 Chain: "I" Number of atoms: 535 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 26, 535 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 26, 532 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "K" Number of atoms: 533 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 26, 533 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "L" Number of atoms: 532 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 26, 532 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "A" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1083 Classifications: {'peptide': 137} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 129} Chain: "B" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1066 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "C" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1066 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "D" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Classifications: {'peptide': 136} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 128} Chain: "E" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1066 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "F" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1066 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "G" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1066 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "H" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1066 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" P A DT I 36 " occ=0.25 ... (18 atoms not shown) pdb=" C6 A DT I 36 " occ=0.25 residue: pdb=" P A DA I 42 " occ=0.25 ... (19 atoms not shown) pdb=" C4 A DA I 42 " occ=0.25 residue: pdb=" P A DA K 20 " occ=0.25 ... (19 atoms not shown) pdb=" C4 A DA K 20 " occ=0.25 residue: pdb=" P A DT K 26 " occ=0.25 ... (18 atoms not shown) pdb=" C6 A DT K 26 " occ=0.25 Time building chain proxies: 2.50, per 1000 atoms: 0.23 Number of scatterers: 10686 At special positions: 0 Unit cell: (98.77, 112.88, 121.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 104 15.00 O 2152 8.00 N 1888 7.00 C 6510 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 312.3 milliseconds 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1990 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 2 sheets defined 47.6% alpha, 11.8% beta 36 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 31 through 36 Processing helix chain 'A' and resid 65 through 77 Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 106 through 113 removed outlier: 4.209A pdb=" N LEU A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'B' and resid 31 through 37 removed outlier: 3.570A pdb=" N ARG B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 77 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'B' and resid 94 through 105 Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'C' and resid 31 through 36 Processing helix chain 'C' and resid 65 through 77 Processing helix chain 'C' and resid 82 through 93 Processing helix chain 'C' and resid 94 through 105 Processing helix chain 'C' and resid 106 through 113 removed outlier: 4.032A pdb=" N LEU C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 129 Processing helix chain 'D' and resid 31 through 36 Processing helix chain 'D' and resid 65 through 78 removed outlier: 3.605A pdb=" N LEU D 78 " --> pdb=" O GLU D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 93 Processing helix chain 'D' and resid 94 through 105 Processing helix chain 'D' and resid 107 through 112 removed outlier: 3.607A pdb=" N LYS D 112 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 132 removed outlier: 4.088A pdb=" N ASP D 130 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE D 132 " --> pdb=" O LEU D 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 65 through 77 Processing helix chain 'E' and resid 82 through 93 Processing helix chain 'E' and resid 94 through 105 Processing helix chain 'E' and resid 106 through 113 removed outlier: 3.868A pdb=" N LEU E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE E 113 " --> pdb=" O THR E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 132 removed outlier: 4.122A pdb=" N ASP E 130 " --> pdb=" O VAL E 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 36 Processing helix chain 'F' and resid 65 through 77 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'F' and resid 94 through 105 Processing helix chain 'F' and resid 107 through 113 removed outlier: 3.871A pdb=" N ILE F 113 " --> pdb=" O THR F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 128 removed outlier: 3.562A pdb=" N ALA F 121 " --> pdb=" O GLY F 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 37 removed outlier: 3.701A pdb=" N ARG G 37 " --> pdb=" O THR G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 77 Processing helix chain 'G' and resid 82 through 93 Processing helix chain 'G' and resid 94 through 105 Processing helix chain 'G' and resid 106 through 113 removed outlier: 4.124A pdb=" N LEU G 110 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE G 113 " --> pdb=" O THR G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 129 Processing helix chain 'H' and resid 31 through 36 Processing helix chain 'H' and resid 65 through 77 Processing helix chain 'H' and resid 82 through 93 Processing helix chain 'H' and resid 94 through 105 Processing helix chain 'H' and resid 107 through 112 removed outlier: 3.501A pdb=" N LYS H 112 " --> pdb=" O SER H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 132 removed outlier: 3.871A pdb=" N ASP H 130 " --> pdb=" O VAL H 126 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 13 removed outlier: 6.766A pdb=" N ILE A 18 " --> pdb=" O ALA A 10 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LYS A 12 " --> pdb=" O HIS A 16 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N HIS A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 24 through 29 current: chain 'A' and resid 58 through 61 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 58 through 61 current: chain 'B' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 24 through 29 current: chain 'B' and resid 58 through 61 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 58 through 61 current: chain 'C' and resid 16 through 21 removed outlier: 3.507A pdb=" N VAL C 24 " --> pdb=" O VAL C 21 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 24 through 29 current: chain 'C' and resid 58 through 61 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 58 through 61 current: chain 'D' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 24 through 29 current: chain 'D' and resid 58 through 61 Processing sheet with id=AA2, first strand: chain 'E' and resid 2 through 13 removed outlier: 3.628A pdb=" N THR E 8 " --> pdb=" O ASP E 20 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE E 18 " --> pdb=" O ALA E 10 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LYS E 12 " --> pdb=" O HIS E 16 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N HIS E 16 " --> pdb=" O LYS E 12 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 24 through 29 current: chain 'E' and resid 58 through 61 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 58 through 61 current: chain 'F' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 24 through 29 current: chain 'F' and resid 57 through 61 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 57 through 61 current: chain 'G' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 24 through 29 current: chain 'G' and resid 58 through 61 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 58 through 61 current: chain 'H' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 24 through 29 current: chain 'H' and resid 57 through 61 356 hydrogen bonds defined for protein. 1047 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 144 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2914 1.34 - 1.45: 2025 1.45 - 1.57: 5887 1.57 - 1.69: 204 1.69 - 1.81: 56 Bond restraints: 11086 Sorted by residual: bond pdb=" N1 DT K 22 " pdb=" C1'A DT K 22 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.28e+01 bond pdb=" C1' DT I 32 " pdb=" N1 DT I 32 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.39e+00 bond pdb=" C3'A DA I 21 " pdb=" C2'A DA I 21 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.06e+00 bond pdb=" N1 DT J 22 " pdb=" C1'A DT J 22 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 8.35e+00 bond pdb=" C3'A DT L 45 " pdb=" C2'A DT L 45 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.23e+00 ... (remaining 11081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.84: 13799 0.84 - 1.68: 1120 1.68 - 2.52: 291 2.52 - 3.35: 197 3.35 - 4.19: 32 Bond angle restraints: 15439 Sorted by residual: angle pdb=" N3 DT K 29 " pdb=" C4 DT K 29 " pdb=" O4 DT K 29 " ideal model delta sigma weight residual 119.90 122.63 -2.73 6.00e-01 2.78e+00 2.07e+01 angle pdb=" N3 DT J 21 " pdb=" C4 DT J 21 " pdb=" O4 DT J 21 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT J 19 " pdb=" C4 DT J 19 " pdb=" O4 DT J 19 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT L 24 " pdb=" C4 DT L 24 " pdb=" O4 DT L 24 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT K 22 " pdb=" C4 DT K 22 " pdb=" O4 DT K 22 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 ... (remaining 15434 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.37: 5939 31.37 - 62.74: 613 62.74 - 94.10: 18 94.10 - 125.47: 1 125.47 - 156.84: 2 Dihedral angle restraints: 6573 sinusoidal: 3484 harmonic: 3089 Sorted by residual: dihedral pdb=" C4'A DA I 20 " pdb=" C3'A DA I 20 " pdb=" O3'A DA I 20 " pdb=" P A DA I 21 " ideal model delta sinusoidal sigma weight residual 220.00 63.16 156.84 1 3.50e+01 8.16e-04 1.50e+01 dihedral pdb=" C4'A DT L 44 " pdb=" C3'A DT L 44 " pdb=" O3'A DT L 44 " pdb=" P A DT L 45 " ideal model delta sinusoidal sigma weight residual 220.00 65.27 154.73 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CA LYS F 129 " pdb=" C LYS F 129 " pdb=" N ASP F 130 " pdb=" CA ASP F 130 " ideal model delta harmonic sigma weight residual -180.00 -162.89 -17.11 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 6570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1349 0.038 - 0.075: 232 0.075 - 0.113: 90 0.113 - 0.151: 114 0.151 - 0.188: 18 Chirality restraints: 1803 Sorted by residual: chirality pdb=" C3'A DA K 13 " pdb=" C4'A DA K 13 " pdb=" O3'A DA K 13 " pdb=" C2'A DA K 13 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" C3'A DA L 34 " pdb=" C4'A DA L 34 " pdb=" O3'A DA L 34 " pdb=" C2'A DA L 34 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" C3'A DA J 25 " pdb=" C4'A DA J 25 " pdb=" O3'A DA J 25 " pdb=" C2'A DA J 25 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.55e-01 ... (remaining 1800 not shown) Planarity restraints: 1598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 38 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO D 39 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 39 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 39 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 113 " 0.021 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO F 114 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO F 114 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 114 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 118 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.35e+00 pdb=" C LYS C 118 " -0.020 2.00e-02 2.50e+03 pdb=" O LYS C 118 " 0.008 2.00e-02 2.50e+03 pdb=" N LYS C 119 " 0.007 2.00e-02 2.50e+03 ... (remaining 1595 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 547 2.73 - 3.27: 9924 3.27 - 3.81: 18441 3.81 - 4.36: 22135 4.36 - 4.90: 36510 Nonbonded interactions: 87557 Sorted by model distance: nonbonded pdb=" O LYS H 118 " pdb=" OE1 GLU H 122 " model vdw 2.182 3.040 nonbonded pdb=" O VAL C 126 " pdb=" NZ LYS G 119 " model vdw 2.183 3.120 nonbonded pdb=" OP1A DA K 30 " pdb=" OG1 THR A 120 " model vdw 2.206 3.040 nonbonded pdb=" O ARG E 123 " pdb=" OE1 GLU E 127 " model vdw 2.241 3.040 nonbonded pdb=" O LYS H 118 " pdb=" N ALA H 121 " model vdw 2.248 3.120 ... (remaining 87552 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 135) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and resid 1 through 135) selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'K' and (resid 12 through 22 or resid 24 through 30 or resid 32 through 3 \ 6)) selection = (chain 'L' and (resid 21 through 24 or resid 26 through 32 or resid 34 through 4 \ 5)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 max=1.00 mean=0.92 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.600 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11086 Z= 0.323 Angle : 0.630 4.193 15439 Z= 0.511 Chirality : 0.049 0.188 1803 Planarity : 0.003 0.052 1598 Dihedral : 20.334 156.839 4583 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.28), residues: 1067 helix: 1.12 (0.25), residues: 507 sheet: -1.52 (0.30), residues: 268 loop : 0.45 (0.42), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 100 TYR 0.007 0.001 TYR C 36 PHE 0.007 0.001 PHE E 132 TRP 0.001 0.000 TRP D 135 HIS 0.002 0.001 HIS B 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.32 (11086) covalent geometry : angle 0.62971 / 0.51 (15439) hydrogen bonds : bond 0.13290 / 14.77 ( 428) hydrogen bonds : angle 5.89058 / 7.32 ( 1191) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: B 70 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8079 (mm-30) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1437 time to fit residues: 41.8060 Evaluate side-chains 174 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 22 ASN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** G 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.179686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.121557 restraints weight = 11354.160| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.11 r_work: 0.3280 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11086 Z= 0.202 Angle : 0.614 8.025 15439 Z= 0.336 Chirality : 0.043 0.305 1803 Planarity : 0.005 0.035 1598 Dihedral : 23.951 154.024 2423 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.18 % Allowed : 6.98 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.27), residues: 1067 helix: 0.93 (0.24), residues: 499 sheet: -1.33 (0.29), residues: 278 loop : 0.67 (0.43), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 77 TYR 0.007 0.001 TYR A 26 PHE 0.011 0.002 PHE D 132 TRP 0.004 0.001 TRP D 135 HIS 0.009 0.002 HIS B 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 (11086) covalent geometry : angle 0.61446 / 0.34 (15439) hydrogen bonds : bond 0.05448 / 6.31 ( 428) hydrogen bonds : angle 4.70602 / 6.04 ( 1191) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 178 time to evaluate : 0.325 Fit side-chains REVERT: B 68 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8378 (mt-10) REVERT: C 112 LYS cc_start: 0.8059 (mptt) cc_final: 0.7758 (mptt) REVERT: C 122 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7154 (mp0) REVERT: D 106 ASP cc_start: 0.7872 (t0) cc_final: 0.7666 (t0) REVERT: E 100 ARG cc_start: 0.7003 (ttp80) cc_final: 0.6613 (ttp80) REVERT: E 109 THR cc_start: 0.7721 (m) cc_final: 0.7520 (p) REVERT: F 94 GLU cc_start: 0.7781 (mp0) cc_final: 0.7571 (mp0) REVERT: F 101 CYS cc_start: 0.6644 (m) cc_final: 0.6386 (m) outliers start: 11 outliers final: 5 residues processed: 183 average time/residue: 0.1574 time to fit residues: 36.9283 Evaluate side-chains 176 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 169 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain H residue 93 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 106 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 61 optimal weight: 0.0980 chunk 14 optimal weight: 0.3980 chunk 81 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 22 ASN ** G 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.179533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.123658 restraints weight = 11479.515| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.27 r_work: 0.3179 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11086 Z= 0.135 Angle : 0.538 6.376 15439 Z= 0.303 Chirality : 0.040 0.284 1803 Planarity : 0.004 0.034 1598 Dihedral : 24.057 155.277 2423 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.50 % Allowed : 7.41 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.27), residues: 1067 helix: 0.93 (0.24), residues: 510 sheet: -1.35 (0.28), residues: 280 loop : 0.62 (0.44), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 67 TYR 0.009 0.001 TYR F 36 PHE 0.009 0.002 PHE F 63 TRP 0.002 0.000 TRP D 135 HIS 0.005 0.001 HIS H 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (11086) covalent geometry : angle 0.53840 / 0.30 (15439) hydrogen bonds : bond 0.04801 / 5.56 ( 428) hydrogen bonds : angle 4.41167 / 5.68 ( 1191) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: B 68 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8232 (mt-10) REVERT: C 112 LYS cc_start: 0.8008 (mptt) cc_final: 0.7766 (mmtm) REVERT: C 122 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: D 106 ASP cc_start: 0.7818 (t0) cc_final: 0.7532 (t0) REVERT: E 65 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8092 (mm-30) REVERT: E 100 ARG cc_start: 0.7125 (ttp80) cc_final: 0.6830 (ttp80) REVERT: E 109 THR cc_start: 0.7739 (m) cc_final: 0.7521 (p) REVERT: F 101 CYS cc_start: 0.6809 (m) cc_final: 0.6558 (m) REVERT: G 93 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7632 (pp) outliers start: 14 outliers final: 5 residues processed: 185 average time/residue: 0.1576 time to fit residues: 37.3812 Evaluate side-chains 176 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 168 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 122 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 13 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 48 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 22 ASN ** G 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.180206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.120412 restraints weight = 11622.200| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.16 r_work: 0.3208 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11086 Z= 0.135 Angle : 0.533 6.420 15439 Z= 0.297 Chirality : 0.040 0.287 1803 Planarity : 0.004 0.032 1598 Dihedral : 24.106 155.188 2423 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.61 % Allowed : 9.34 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.27), residues: 1067 helix: 1.11 (0.24), residues: 496 sheet: -1.38 (0.28), residues: 280 loop : 0.75 (0.42), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 67 TYR 0.005 0.001 TYR F 36 PHE 0.008 0.002 PHE D 132 TRP 0.002 0.000 TRP D 135 HIS 0.005 0.001 HIS H 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (11086) covalent geometry : angle 0.53254 / 0.30 (15439) hydrogen bonds : bond 0.04635 / 5.40 ( 428) hydrogen bonds : angle 4.25708 / 5.50 ( 1191) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 0.368 Fit side-chains REVERT: B 68 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8363 (mt-10) REVERT: C 17 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8170 (mt) REVERT: C 112 LYS cc_start: 0.8113 (mptt) cc_final: 0.7732 (mmtm) REVERT: C 122 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7113 (mp0) REVERT: D 106 ASP cc_start: 0.7806 (t0) cc_final: 0.7431 (t0) REVERT: E 65 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8145 (mm-30) REVERT: E 100 ARG cc_start: 0.7048 (ttp80) cc_final: 0.6729 (ttp80) REVERT: E 109 THR cc_start: 0.7755 (m) cc_final: 0.7526 (p) REVERT: E 123 ARG cc_start: 0.8059 (mtm-85) cc_final: 0.7374 (mtp85) REVERT: F 101 CYS cc_start: 0.6670 (m) cc_final: 0.6435 (m) REVERT: G 93 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7538 (pp) outliers start: 15 outliers final: 8 residues processed: 187 average time/residue: 0.1553 time to fit residues: 37.4342 Evaluate side-chains 187 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 122 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 80 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 90 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 22 ASN C 79 ASN ** G 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.180153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.116732 restraints weight = 11538.679| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.13 r_work: 0.3218 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11086 Z= 0.134 Angle : 0.532 6.150 15439 Z= 0.295 Chirality : 0.040 0.286 1803 Planarity : 0.004 0.031 1598 Dihedral : 24.131 155.541 2423 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.26 % Allowed : 9.45 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.27), residues: 1067 helix: 1.13 (0.24), residues: 496 sheet: -1.38 (0.28), residues: 280 loop : 0.78 (0.42), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 77 TYR 0.007 0.001 TYR F 36 PHE 0.007 0.002 PHE F 63 TRP 0.002 0.000 TRP D 135 HIS 0.006 0.001 HIS H 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (11086) covalent geometry : angle 0.53157 / 0.30 (15439) hydrogen bonds : bond 0.04525 / 5.26 ( 428) hydrogen bonds : angle 4.17661 / 5.40 ( 1191) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.374 Fit side-chains REVERT: B 68 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8367 (mt-10) REVERT: C 17 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8170 (mt) REVERT: C 112 LYS cc_start: 0.8128 (mptt) cc_final: 0.7746 (mmtm) REVERT: C 122 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: D 106 ASP cc_start: 0.7837 (t0) cc_final: 0.7453 (t0) REVERT: D 129 LYS cc_start: 0.7926 (tppt) cc_final: 0.7676 (tppt) REVERT: E 32 MET cc_start: 0.7904 (mmm) cc_final: 0.7521 (mmm) REVERT: E 65 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8157 (mm-30) REVERT: E 100 ARG cc_start: 0.7122 (ttp80) cc_final: 0.6801 (ttp80) REVERT: F 96 ASP cc_start: 0.8129 (p0) cc_final: 0.7451 (p0) REVERT: F 97 GLU cc_start: 0.7610 (mp0) cc_final: 0.6914 (mp0) REVERT: F 101 CYS cc_start: 0.6760 (m) cc_final: 0.6532 (m) REVERT: G 93 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7537 (pp) outliers start: 21 outliers final: 12 residues processed: 190 average time/residue: 0.1547 time to fit residues: 37.8127 Evaluate side-chains 186 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 122 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 101 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 6 optimal weight: 40.0000 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 0.4980 chunk 95 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 110 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 22 ASN G 58 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.180556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.121993 restraints weight = 11613.963| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.37 r_work: 0.3127 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11086 Z= 0.136 Angle : 0.530 6.169 15439 Z= 0.293 Chirality : 0.040 0.286 1803 Planarity : 0.004 0.031 1598 Dihedral : 24.140 155.597 2423 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.04 % Allowed : 10.63 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.27), residues: 1067 helix: 1.15 (0.24), residues: 496 sheet: -1.36 (0.28), residues: 280 loop : 0.81 (0.42), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 67 TYR 0.006 0.001 TYR F 36 PHE 0.008 0.002 PHE D 132 TRP 0.003 0.000 TRP D 135 HIS 0.005 0.001 HIS H 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (11086) covalent geometry : angle 0.52959 / 0.29 (15439) hydrogen bonds : bond 0.04456 / 5.17 ( 428) hydrogen bonds : angle 4.13923 / 5.35 ( 1191) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.382 Fit side-chains REVERT: B 68 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8240 (mt-10) REVERT: C 17 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8130 (mt) REVERT: C 112 LYS cc_start: 0.8093 (mptt) cc_final: 0.7665 (mmtm) REVERT: C 122 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7143 (mp0) REVERT: D 106 ASP cc_start: 0.7845 (t0) cc_final: 0.7462 (t0) REVERT: D 129 LYS cc_start: 0.7905 (tppt) cc_final: 0.7674 (tppt) REVERT: E 32 MET cc_start: 0.7846 (mmm) cc_final: 0.7445 (mmm) REVERT: E 65 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8055 (mm-30) REVERT: E 100 ARG cc_start: 0.7182 (ttp80) cc_final: 0.6933 (tmm160) REVERT: F 101 CYS cc_start: 0.6805 (m) cc_final: 0.6584 (m) REVERT: G 93 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7586 (pp) outliers start: 19 outliers final: 10 residues processed: 182 average time/residue: 0.1587 time to fit residues: 37.0822 Evaluate side-chains 183 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 122 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 60 optimal weight: 0.2980 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 13 optimal weight: 0.4980 chunk 52 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.180624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.115432 restraints weight = 11499.040| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.12 r_work: 0.3207 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11086 Z= 0.148 Angle : 0.541 6.181 15439 Z= 0.296 Chirality : 0.040 0.284 1803 Planarity : 0.004 0.032 1598 Dihedral : 24.153 155.742 2423 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.83 % Allowed : 10.96 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.27), residues: 1067 helix: 1.12 (0.24), residues: 496 sheet: -1.35 (0.28), residues: 280 loop : 0.78 (0.42), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 67 TYR 0.006 0.001 TYR F 36 PHE 0.009 0.002 PHE D 132 TRP 0.003 0.001 TRP D 135 HIS 0.006 0.001 HIS H 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (11086) covalent geometry : angle 0.54108 / 0.30 (15439) hydrogen bonds : bond 0.04486 / 5.20 ( 428) hydrogen bonds : angle 4.15586 / 5.38 ( 1191) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.506 Fit side-chains REVERT: B 68 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8386 (mt-10) REVERT: C 17 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8185 (mt) REVERT: C 101 CYS cc_start: 0.7545 (OUTLIER) cc_final: 0.6727 (m) REVERT: C 112 LYS cc_start: 0.8099 (mptt) cc_final: 0.7670 (mmtm) REVERT: C 122 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: D 106 ASP cc_start: 0.7894 (t0) cc_final: 0.7485 (t0) REVERT: D 129 LYS cc_start: 0.7868 (tppt) cc_final: 0.7235 (tptt) REVERT: E 32 MET cc_start: 0.7964 (mmm) cc_final: 0.7545 (mmm) REVERT: E 65 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8148 (mm-30) REVERT: E 100 ARG cc_start: 0.7139 (ttp80) cc_final: 0.6889 (tmm160) REVERT: F 101 CYS cc_start: 0.6763 (m) cc_final: 0.6521 (m) REVERT: G 93 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7577 (pp) outliers start: 17 outliers final: 10 residues processed: 185 average time/residue: 0.1534 time to fit residues: 36.3640 Evaluate side-chains 187 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 101 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 122 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 13 optimal weight: 0.4980 chunk 92 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 103 optimal weight: 0.0980 chunk 55 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.180965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.115915 restraints weight = 11560.180| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.13 r_work: 0.3193 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11086 Z= 0.133 Angle : 0.528 5.886 15439 Z= 0.292 Chirality : 0.040 0.285 1803 Planarity : 0.004 0.031 1598 Dihedral : 24.118 155.667 2423 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.72 % Allowed : 11.17 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.27), residues: 1067 helix: 1.13 (0.24), residues: 496 sheet: -1.35 (0.28), residues: 280 loop : 0.84 (0.42), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 67 TYR 0.006 0.001 TYR F 36 PHE 0.007 0.002 PHE B 63 TRP 0.003 0.000 TRP D 135 HIS 0.004 0.001 HIS H 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (11086) covalent geometry : angle 0.52845 / 0.29 (15439) hydrogen bonds : bond 0.04327 / 5.01 ( 428) hydrogen bonds : angle 4.13559 / 5.34 ( 1191) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.398 Fit side-chains REVERT: A 65 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8279 (mm-30) REVERT: B 68 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8275 (mt-10) REVERT: C 17 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8154 (mt) REVERT: C 32 MET cc_start: 0.8009 (mmt) cc_final: 0.7747 (mmt) REVERT: C 101 CYS cc_start: 0.7485 (OUTLIER) cc_final: 0.6689 (m) REVERT: C 112 LYS cc_start: 0.8115 (mptt) cc_final: 0.7817 (tptp) REVERT: C 122 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: D 106 ASP cc_start: 0.7880 (t0) cc_final: 0.7466 (t0) REVERT: D 129 LYS cc_start: 0.7867 (tppt) cc_final: 0.7638 (tptt) REVERT: E 65 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8111 (mm-30) REVERT: E 100 ARG cc_start: 0.7198 (ttp80) cc_final: 0.6947 (tmm160) REVERT: E 123 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.7319 (mtp85) REVERT: E 127 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6819 (mt-10) REVERT: F 101 CYS cc_start: 0.6687 (m) cc_final: 0.6445 (m) REVERT: G 93 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7502 (pp) outliers start: 16 outliers final: 9 residues processed: 185 average time/residue: 0.1607 time to fit residues: 38.0421 Evaluate side-chains 176 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 101 CYS Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 122 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 55 optimal weight: 0.4980 chunk 100 optimal weight: 0.3980 chunk 80 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 89 optimal weight: 0.0870 chunk 67 optimal weight: 1.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.181819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.116948 restraints weight = 11573.384| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.13 r_work: 0.3207 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11086 Z= 0.118 Angle : 0.519 5.691 15439 Z= 0.289 Chirality : 0.039 0.286 1803 Planarity : 0.004 0.030 1598 Dihedral : 24.073 155.893 2423 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.61 % Allowed : 11.28 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.27), residues: 1067 helix: 1.15 (0.24), residues: 498 sheet: -1.36 (0.28), residues: 280 loop : 0.85 (0.42), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 67 TYR 0.005 0.000 TYR F 36 PHE 0.007 0.002 PHE F 63 TRP 0.002 0.000 TRP D 135 HIS 0.003 0.001 HIS H 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (11086) covalent geometry : angle 0.51900 / 0.29 (15439) hydrogen bonds : bond 0.04215 / 4.88 ( 428) hydrogen bonds : angle 4.10994 / 5.30 ( 1191) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 0.366 Fit side-chains REVERT: A 65 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8287 (mm-30) REVERT: C 17 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8142 (mt) REVERT: C 32 MET cc_start: 0.7972 (mmt) cc_final: 0.7701 (mmt) REVERT: C 101 CYS cc_start: 0.7455 (OUTLIER) cc_final: 0.6696 (m) REVERT: C 112 LYS cc_start: 0.8128 (mptt) cc_final: 0.7681 (mmtm) REVERT: C 122 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: D 106 ASP cc_start: 0.7866 (t0) cc_final: 0.7483 (t0) REVERT: D 129 LYS cc_start: 0.7857 (tppt) cc_final: 0.7630 (tptt) REVERT: E 32 MET cc_start: 0.7873 (mmm) cc_final: 0.7412 (mmm) REVERT: E 65 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8128 (mm-30) REVERT: E 100 ARG cc_start: 0.7199 (ttp80) cc_final: 0.6946 (tmm160) REVERT: E 123 ARG cc_start: 0.8034 (mtm-85) cc_final: 0.7320 (mtp85) REVERT: F 97 GLU cc_start: 0.7572 (mp0) cc_final: 0.6974 (mp0) REVERT: F 101 CYS cc_start: 0.6667 (m) cc_final: 0.6429 (m) REVERT: G 93 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7518 (pp) outliers start: 15 outliers final: 10 residues processed: 186 average time/residue: 0.1586 time to fit residues: 37.8793 Evaluate side-chains 191 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 101 CYS Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 122 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 63 optimal weight: 0.0670 chunk 55 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 0 optimal weight: 40.0000 chunk 76 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.180998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.116177 restraints weight = 11448.456| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.11 r_work: 0.3196 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11086 Z= 0.135 Angle : 0.535 6.055 15439 Z= 0.293 Chirality : 0.040 0.283 1803 Planarity : 0.004 0.038 1598 Dihedral : 24.076 156.020 2423 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.61 % Allowed : 11.17 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.27), residues: 1067 helix: 1.12 (0.24), residues: 498 sheet: -1.34 (0.28), residues: 280 loop : 0.85 (0.42), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 67 TYR 0.005 0.001 TYR F 36 PHE 0.008 0.002 PHE D 132 TRP 0.003 0.000 TRP D 135 HIS 0.004 0.001 HIS H 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (11086) covalent geometry : angle 0.53504 / 0.29 (15439) hydrogen bonds : bond 0.04320 / 5.00 ( 428) hydrogen bonds : angle 4.11075 / 5.32 ( 1191) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 0.348 Fit side-chains REVERT: C 17 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8154 (mt) REVERT: C 32 MET cc_start: 0.7997 (mmt) cc_final: 0.7723 (mmt) REVERT: C 101 CYS cc_start: 0.7466 (OUTLIER) cc_final: 0.6710 (m) REVERT: C 112 LYS cc_start: 0.8156 (mptt) cc_final: 0.7759 (mmtm) REVERT: C 122 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: D 106 ASP cc_start: 0.7861 (t0) cc_final: 0.7483 (t0) REVERT: D 129 LYS cc_start: 0.7872 (tppt) cc_final: 0.7310 (tptt) REVERT: E 32 MET cc_start: 0.7868 (mmm) cc_final: 0.7415 (mmm) REVERT: E 65 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8170 (mm-30) REVERT: E 100 ARG cc_start: 0.7245 (ttp80) cc_final: 0.6995 (tmm160) REVERT: E 123 ARG cc_start: 0.8040 (mtm-85) cc_final: 0.7342 (mtp85) REVERT: E 127 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6879 (mt-10) REVERT: F 97 GLU cc_start: 0.7582 (mp0) cc_final: 0.7048 (mp0) REVERT: F 101 CYS cc_start: 0.6681 (m) cc_final: 0.6460 (m) REVERT: G 93 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7546 (pp) REVERT: H 123 ARG cc_start: 0.7703 (mmm-85) cc_final: 0.7469 (mmm-85) outliers start: 15 outliers final: 10 residues processed: 192 average time/residue: 0.1615 time to fit residues: 39.7196 Evaluate side-chains 196 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 101 CYS Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 122 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 2 optimal weight: 30.0000 chunk 66 optimal weight: 0.5980 chunk 65 optimal weight: 0.4980 chunk 70 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 chunk 18 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 22 ASN H 22 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.181274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.116272 restraints weight = 11565.156| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.13 r_work: 0.3197 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11086 Z= 0.131 Angle : 0.535 5.921 15439 Z= 0.294 Chirality : 0.040 0.284 1803 Planarity : 0.004 0.034 1598 Dihedral : 24.057 156.067 2423 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.61 % Allowed : 11.28 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.27), residues: 1067 helix: 1.12 (0.24), residues: 498 sheet: -1.34 (0.28), residues: 280 loop : 0.87 (0.43), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 67 TYR 0.005 0.001 TYR F 36 PHE 0.007 0.002 PHE E 132 TRP 0.003 0.000 TRP D 135 HIS 0.004 0.001 HIS H 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (11086) covalent geometry : angle 0.53549 / 0.29 (15439) hydrogen bonds : bond 0.04280 / 4.95 ( 428) hydrogen bonds : angle 4.11256 / 5.32 ( 1191) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3614.34 seconds wall clock time: 62 minutes 18.04 seconds (3738.04 seconds total)